Spiking neuron model of the basal ganglia (Humphries et al 2006)

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A spiking neuron model of the basal ganglia (BG) circuit (striatum, STN, GP, SNr). Includes: parallel anatomical channels; tonic dopamine; dopamine receptors in striatum, STN, and GP; burst-firing in STN; GABAa, AMPA, and NMDA currents; effects of synaptic location. Model demonstrates selection and switching of input signals. Replicates experimental data on changes in slow-wave (<1 Hz) and gamma-band oscillations within BG nuclei following lesions and pharmacological manipulations.
1 . Humphries MD, Stewart RD, Gurney KN (2006) A physiologically plausible model of action selection and oscillatory activity in the basal ganglia. J Neurosci 26:12921-42 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Basal ganglia;
Cell Type(s): Neostriatum spiny direct pathway neuron; Subthalamus nucleus projection neuron; Globus pallidus neuron; Abstract integrate-and-fire leaky neuron;
Gap Junctions:
Receptor(s): Dopaminergic Receptor;
Transmitter(s): Dopamine; Gaba; Glutamate;
Simulation Environment: MATLAB;
Model Concept(s): Oscillations; Parkinson's; Action Selection/Decision Making; Sleep; Rebound firing;
Implementer(s): Humphries, Mark D [m.d.humphries at shef.ac.uk];
Search NeuronDB for information about:  Neostriatum spiny direct pathway neuron; Dopaminergic Receptor; Dopamine; Gaba; Glutamate;
function single_run5_2d()

% run a single model and postprocess it

[a host] = system('hostname');
fprintf(['\n' host '\n']);

%%% set requisite paths!
if findstr(host, 'iceberg'); % on iceberg
     fprintf('\n On ICEBERG \n');
     system_os = 'unix';
     ice_path1 = genpath('/home1/pc/pc1mdh/BG spiking model');
     ice_path2 = genpath('/home1/pc/pc1mdh/Matlab Tools');
     path(path, ice_path1);
     path(path, ice_path2);
elseif (findstr(host, 'node') | findstr(host,'ace')) % on ACE
     system_os = 'unix';
     ace_path1 = genpath('/home/mark/SpikingModel');
     path(path, ace_path1);
     fprintf('\n On ACE \n');
     system_os = 'xp';
     fprintf('\n On XP \n');

%%%% always need all of these parameters %%%%%%
n_batches = 50;
n_models = 6; % 6
structures = {'STN' 'GPe'};
n_cells_per_structure = [3 3];
extract_thresh = 0;

pathroot = ['/home/mark/SpikingModel/ResultsArchive/LFO-urethane/NoSTN_DA/ConditionD/'];  % path to save files
pars_file = 'pars5_2d';
flags_file = 'sum_flags45';

exp_name = 'LFO_5_2d';
type = 'SG';


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